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fix: don't enforce serializeNulls, but DO still ensure null is still #42

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merged 4 commits into from
Jul 12, 2024
Merged

fix: don't enforce serializeNulls, but DO still ensure null is still #42

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4546772
fix: don't enforce `serializeNulls`, but DO still ensure `null` is still
cmhulbert Jun 6, 2024
550782d
fix: don't require gsonBuilder to `serializeNull`
cmhulbert Jun 6, 2024
124c75d
fix(test): don't ignore input GsonBuilder
cmhulbert Jun 6, 2024
88a88ff
fix(test): serializeNulls for consistency between Cached and non-cach…
cmhulbert Jun 6, 2024
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22 changes: 21 additions & 1 deletion src/main/java/org/janelia/saalfeldlab/n5/zarr/ZArrayAttributes.java
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Expand Up @@ -34,6 +34,8 @@
import java.util.HashMap;
import java.util.List;

import com.google.gson.JsonSerializationContext;
import com.google.gson.JsonSerializer;
import org.janelia.saalfeldlab.n5.DataType;
import org.janelia.saalfeldlab.n5.RawCompression;

Expand Down Expand Up @@ -222,7 +224,7 @@ public Collection<Filter> getFilters() {

public static JsonAdapter jsonAdapter = new JsonAdapter();

public static class JsonAdapter implements JsonDeserializer<ZArrayAttributes> {
public static class JsonAdapter implements JsonDeserializer<ZArrayAttributes>, JsonSerializer<ZArrayAttributes> {

@Override
public ZArrayAttributes deserialize(JsonElement json, Type typeOfT, JsonDeserializationContext context) throws JsonParseException {
Expand All @@ -249,5 +251,23 @@ public ZArrayAttributes deserialize(JsonElement json, Type typeOfT, JsonDeserial
}
}

@Override
public JsonElement serialize(ZArrayAttributes src, Type typeOfSrc, JsonSerializationContext context) {

final JsonObject jsonObject = new JsonObject();

jsonObject.addProperty("zarr_format", src.getZarrFormat());
jsonObject.add("shape", context.serialize(src.getShape()));
jsonObject.add("chunks", context.serialize(src.getChunks()));

jsonObject.add("dtype", context.serialize(src.getDType().toString()));
jsonObject.add("compressor", context.serialize(src.getCompressor()));
jsonObject.addProperty("fill_value", src.getFillValue());
jsonObject.addProperty("order", src.getOrder());
jsonObject.addProperty("dimension_separator", src.getDimensionSeparator());
jsonObject.add("filters", context.serialize(src.getFilters()));

return jsonObject;
}
}
}
21 changes: 18 additions & 3 deletions src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrCompressor.java
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Expand Up @@ -28,15 +28,17 @@
*/
package org.janelia.saalfeldlab.n5.zarr;

import java.io.IOException;
import java.lang.reflect.Field;
import java.lang.reflect.Type;
import java.util.AbstractMap.SimpleImmutableEntry;
import java.util.Map;
import java.util.stream.Collectors;
import java.util.stream.Stream;

import com.google.gson.JsonNull;
import com.google.gson.JsonSerializer;
import com.google.gson.TypeAdapter;
import com.google.gson.stream.JsonReader;
import com.google.gson.stream.JsonWriter;
import org.janelia.saalfeldlab.n5.Bzip2Compression;
import org.janelia.saalfeldlab.n5.Compression;
import org.janelia.saalfeldlab.n5.GzipCompression;
Expand Down Expand Up @@ -297,5 +299,18 @@ public ZarrCompressor deserialize(final JsonElement json, final Type typeOfT, fi
}
}

JsonSerializer<Raw> rawNullAdapter = (src, typeOfSrc, context) -> JsonNull.INSTANCE;
TypeAdapter<Raw> rawNullAdapter = new TypeAdapter<Raw>() {

@Override public void write(JsonWriter out, Raw value) throws IOException {
final boolean serializeNull = out.getSerializeNulls();
out.setSerializeNulls(true);
out.nullValue();
out.setSerializeNulls(serializeNull);
}

@Override public Raw read(JsonReader in) {

return new Raw();
}
};
}
3 changes: 1 addition & 2 deletions src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrKeyValueReader.java
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Expand Up @@ -525,7 +525,7 @@ protected JsonElement zarrToN5DatasetAttributes(final JsonElement elem ) {
attrs.addProperty(DatasetAttributes.DATA_TYPE_KEY, zattrs.getDType().getDataType().toString());

final JsonElement e = attrs.get(ZArrayAttributes.compressorKey);
if (e == JsonNull.INSTANCE) {
if (e == JsonNull.INSTANCE || e == null) {
attrs.add(DatasetAttributes.COMPRESSION_KEY, gson.toJsonTree(new RawCompression()));
} else {
attrs.add(DatasetAttributes.COMPRESSION_KEY, gson.toJsonTree(
Expand Down Expand Up @@ -863,7 +863,6 @@ protected static GsonBuilder addTypeAdapters(final GsonBuilder gsonBuilder) {
gsonBuilder.registerTypeAdapter(ZArrayAttributes.class, ZArrayAttributes.jsonAdapter);
gsonBuilder.registerTypeHierarchyAdapter(Filter.class, Filter.jsonAdapter);
gsonBuilder.disableHtmlEscaping();
gsonBuilder.serializeNulls();

return gsonBuilder;
}
Expand Down
16 changes: 11 additions & 5 deletions src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrKeyValueWriter.java
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Expand Up @@ -27,7 +27,9 @@

import java.io.IOException;
import java.io.OutputStream;
import java.io.Writer;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.function.Supplier;
import java.util.stream.Collectors;
Expand Down Expand Up @@ -258,8 +260,10 @@ else if (getCache().isGroup(normalPath, ZGROUP_FILE)) {
// These three lines are preferable to setDatasetAttributes because they
// are more efficient wrt caching
final ZArrayAttributes zarray = createZArrayAttributes(datasetAttributes);
final JsonElement attributes = gson.toJsonTree(zarray.asMap());
writeJsonResource(normalPath, ZARRAY_FILE, attributes);
final HashMap<String, Object> zarrayMap = zarray.asMap();
final JsonElement attributes = gson.toJsonTree(zarrayMap);
writeJsonResource(normalPath, ZARRAY_FILE, zarrayMap);

if( wasGroup )
deleteJsonResource(normalPath, ZGROUP_FILE );

Expand Down Expand Up @@ -416,14 +420,16 @@ protected void deleteJsonResource(final String normalPath, final String jsonName
protected void writeJsonResource(
final String normalPath,
final String jsonName,
final JsonElement attributes) throws N5Exception {
final Object attributes) throws N5Exception {

if (attributes == null)
return;

final String absolutePath = keyValueAccess.compose(uri, normalPath, jsonName);
try (final LockedChannel lock = keyValueAccess.lockForWriting(absolutePath)) {
GsonUtils.writeAttributes(lock.newWriter(), attributes, gson);
final Writer writer = lock.newWriter();
gson.toJson(attributes, writer);
writer.flush();
} catch (final Throwable e) {
throw new N5IOException("Failed to write " + absolutePath, e);
}
Expand All @@ -436,7 +442,7 @@ protected void writeZArray(
if (attributes == null)
return;

writeJsonResource(normalGroupPath, ZARRAY_FILE, attributes);
writeJsonResource(normalGroupPath, ZARRAY_FILE, gson.fromJson(attributes, ZArrayAttributes.class));
if (cacheMeta())
cache.updateCacheInfo(normalGroupPath, ZARRAY_FILE, attributes);
}
Expand Down
5 changes: 2 additions & 3 deletions src/test/java/org/janelia/saalfeldlab/n5/zarr/N5ZarrTest.java
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Expand Up @@ -146,7 +146,7 @@ protected N5Writer createTempN5Writer(
final String dimensionSeparator,
final boolean mapN5DatasetAttributes) throws IOException {

return createTempN5Writer(location, new GsonBuilder(), dimensionSeparator, mapN5DatasetAttributes, false);
return createTempN5Writer(location, gsonBuilder, dimensionSeparator, mapN5DatasetAttributes, false);
}

protected N5Writer createTempN5Writer(
Expand Down Expand Up @@ -778,7 +778,7 @@ public void testAttributes() {
public void testAttributeMapping() {

// attribute mapping on by default
try (final N5Writer n5 = createTempN5Writer()) {
try (final N5Writer n5 = createTempN5Writer(tempN5Location(), new GsonBuilder().serializeNulls())) {

n5.createDataset(datasetName, dimensions, blockSize, DataType.UINT64, getCompressions()[0]);

Expand Down Expand Up @@ -832,7 +832,6 @@ public void testAttributeMapping() {
n5Compression = n5.getAttribute(datasetName, DatasetAttributes.COMPRESSION_KEY, Compression.class);
assertEquals(rawCompression, n5Compression);
assertThrows(N5Exception.N5ClassCastException.class, () -> n5.getAttribute(datasetName, ZArrayAttributes.compressorKey, ZarrCompressor.class));

final GzipCompression gzipCompression = new GzipCompression();
n5.setAttribute(datasetName, DatasetAttributes.COMPRESSION_KEY, gzipCompression);
zarrCompression = n5.getAttribute(datasetName, ZArrayAttributes.compressorKey, ZarrCompressor.class);
Expand Down
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